Mutation spectrum per sample (M matrix)

Heatmap to visualize mutational spectra across all samples

Combined mutation spectrum

These plots shows the total number of observations in each subtype, combined across all samples

All samples

Signature loadings (H matrix)

Describes how each mutation subtype is loaded into the r signatures

## # A tibble: 3 x 4
##   rowname        S1        S2        S3
##     <chr>     <dbl>     <dbl>     <dbl>
## 1      S1        NA 0.9783121 0.8396949
## 2      S2 0.9783121        NA 0.7716099
## 3      S3 0.8396949 0.7716099        NA
## `mutate_each()` is deprecated.
## Use `mutate_all()`, `mutate_at()` or `mutate_if()` instead.
## To map `funs` over a selection of variables, use `mutate_at()`

Signature contributions per sample (W matrix)

Proportion each signature contributes to the mutation spectrum in each individual sample

Signature contributions per kept samples (W matrix)

Proportion each signature contributes to the mutation spectrum in each individual sample

Signature contributions per dropped samples (W matrix)

Proportion each signature contributes to the mutation spectrum in each individual sample

Outlier analysis

This plot shows detailed information about the top 50 IDs with the largest root mean squared error. The left panel shows the RMSE values, and each sample is colored by the mutation signature with the largest contribution.

The contributions of each mutation signature for each of these samples are broken down in the right panel. If the sample was identified as an outlier (by having a signature contribution >2 standard deviations from the mean), it is marked with a star.

Error profiles for top 20 outliers

Interactive heatmap of error profiles

IDs with similar error profiles are grouped together using hierarchical clustering.

## We recommend that you use the dev version of ggplot2 with `ggplotly()`
## Install it with: `devtools::install_github('hadley/ggplot2')`
## We recommend that you use the dev version of ggplot2 with `ggplotly()`
## Install it with: `devtools::install_github('hadley/ggplot2')`
## Warning: Specifying width/height in layout() is now deprecated.
## Please specify in ggplotly() or plot_ly()